title: 2-15-05_time_course_part_one_+dox_36hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59307.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 36 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 10:23:30; Parameter PMT Volts = 580; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203001; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 10:23:30; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567804; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 + dox for 36hr

tag: 1325 + dox for 36hr


title: 2-15-05_time_course_part_one_+dox_0hr

status: Public on Aug 28 2008

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59301.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 0 h

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 10:51:49; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203028; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 10:51:49; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567832; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm), default computed normalization procedure, see SMD website

molecule: total RNA

organism: Mus musculus

source_name: reference 30ug

label_protocol: not provided

extract_protocol: not provided

tag: reference 30ug

source_name: dox 0hr 30ug

tag: dox 0hr 30ug


title: PrP-null KO 14 days post-Dox 3

status: Public on Aug 27 2008

city: Winnipeg

first: Debra

last: Parchaliuk

state: Manitoba

address: 1015 Arlington Street

department: Prion Diseases Program

country: Canada

institute: Public Health Agency of Canada

description: Uninfected aged-matched mice used as control

hyb_protocol: A total of 16,315 cDNA expressed sequence tags were spotted in duplicate onto CMT-GAPS Gamma Amino Propyl Silane coated glass slides (Corning) using the Virtek Chip Writer.   5ug of both reference (WT) and experimental (KO and HQK) Alexa Flour labeled aRNA were used in each competitive hybridization.   Each labeled aRNA was resuspended in 35ml DIG Easy HybTM hybridization buffer (Roche) containing 20mg mouse cot1 DNA and 20 mg poly(A)-DNA to block non-specific hybridization.   Three biological replicate samples from each of the reference and experimental groups were combined, heated for 5 minutes at 95°C, then cooled and maintained at 42°C.  The labeled aRNA sample mixtures were added to a BMAP-MSV microarray and incubated in the dark at 42°C overnight to competitively hybridize to reference and experimental samples. The number of slides hybridized in each experiment corresponded to the number of biological replicates in each group of experimental interest.  Following hybridization, the slides were washed once in low stringency wash buffer (1X SSC, 0.2% SDS) preheated to 42°C for 5 minutes, once in high stringency wash buffer (0.1X SSC, and 0.2%SDS) for 5 minutes at room temperature, and then once in 0.1X SSC for 5 minutes at room temperature.

scan_protocol: The slides were analyzed in two channels using the Agilent HT microarray scanner (Agilent).

data_processing: Raw, background and net intensity values were collected using Array-Pro software (MediaCybernetics). In order to account for variation in fluorescence, LOWESS sub-grid normalization was performed by Gene Traffic software (Iobion), and the subsequent normalized log2 ratios obtained.

label: AlexaFluor 555

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications.  In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis.  In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified.  10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 555 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour.  Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

extract_protocol: Total RNA was isolated from frozen skeletal muscle using the Qiagen RNeasy skeletal muscle RNA isolation kit (Qiagen) following manufacturers’ specifications.  The total RNA preparations were further treated with Turbo DNA-Free DNase (Ambion) to remove residual genomic DNA contamination, and examined with an Agilent 2100 Bioanalyzer (Agilent) for purity and quantity.

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

tag: Line

value: Wild-type

tag: Treatment

value: 14 days post Dox admin

label: AlexaFluor 647

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications.  In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis.  In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified.  10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 647 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour.  Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

tag: Line:PrP-null (KO)


title: PrP overexpression HQK-2 30 days post-Dox

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: 30 days post Dox admin

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: Transgenic HQK


title: PrP-null KO 7 days post-Dox 1 DS

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: 7 days post Dox admin

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-1 14 days post-Dox DS

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-2 14 days post-Dox DS

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP-null KO 14 days post-Dox 1


title: PrP-null KO 14 days post-Dox 2


title: PrP overexpression HQK-3 14 days post-Dox


title: PrP overexpression HQK-2 30 days post-Dox DS

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP-null KO 14 days post-Dox 2 DS


title: PrP overexpression HQK-2 14 days post-Dox


title: PrP overexpression HQK-1 14 days post-Dox


title: PrP-null KO 7 days post-Dox 3

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-1 7 days post-Dox

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-2 7 days post-Dox


title: PrP-null KO 7 days post-Dox 3 DS


title: PrP-null KO 4 days post-Dox 2

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: 4 days post Dox admin

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-1 7 days post-Dox DS


title: PrP-null KO 4 days post-Dox 1

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP-null KO 7 days post-Dox 1


title: PrP overexpression HQK-3 14 days post-Dox DS


title: PrP overexpression HQK-3 7 days post-Dox


title: PrP-null KO 30 days post-Dox 1 DS

hyb_protocol: A total of 16,315 cDNA expressed sequence tags were spotted in duplicate onto CMT-GAPS Gamma Amino Propyl Silane coated glass slides (Corning) using the Virtek Chip Writer. 5ug of both reference (WT) and experimental (KO and HQK) Alexa Flour labeled aRNA were used in each competitive hybridization. Each labeled aRNA was resuspended in 35ml DIG Easy HybTM hybridization buffer (Roche) containing 20mg mouse cot1 DNA and 20 mg poly(A)-DNA to block non-specific hybridization. Three biological replicate samples from each of the reference and experimental groups were combined, heated for 5 minutes at 95°C, then cooled and maintained at 42°C. The labeled aRNA sample mixtures were added to a BMAP-MSV microarray and incubated in the dark at 42°C overnight to competitively hybridize to reference and experimental samples. The number of slides hybridized in each experiment corresponded to the number of biological replicates in each group of experimental interest. Following hybridization, the slides were washed once in low stringency wash buffer (1X SSC, 0.2% SDS) preheated to 42°C for 5 minutes, once in high stringency wash buffer (0.1X SSC, and 0.2%SDS) for 5 minutes at room temperature, and then once in 0.1X SSC for 5 minutes at room temperature.

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications. In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis. In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified. 10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 647 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour. Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

extract_protocol: Total RNA was isolated from frozen skeletal muscle using the Qiagen RNeasy skeletal muscle RNA isolation kit (Qiagen) following manufacturers’ specifications. The total RNA preparations were further treated with Turbo DNA-Free DNase (Ambion) to remove residual genomic DNA contamination, and examined with an Agilent 2100 Bioanalyzer (Agilent) for purity and quantity.


title: PrP-null KO 4 days post-Dox 3 DS


title: PrP-null KO 4 days post-Dox 2 DS


title: PrP-null KO 4 days post-Dox 1 DS

treatment_protocol: Prp null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP-null KO 4 days post-Dox 3


title: PrP overexpression HQK-2 7 days post-Dox DS


title: PrP overexpression HQK-1 4 days post-Dox DS

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-1 4 days post-Dox


title: PrP overexpression HQK-3 4 days post-Dox DS

treatment_protocol: HQK transgenic  mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP overexpression HQK-2 4 days post-Dox DS


title: PrP-null KO 30 days post-Dox 3


title: PrP overexpression HQK-2 4 days post-Dox


title: PrP overexpression HQK-3 0 days post-Dox

description: Untreated aged-matched mice used for control

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications.  In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis.  In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified.  10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 555  in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour.  Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 following administration of Dox. The subsequent tissue was used for total RNA extraction.

value: O days post Dox admin

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 following administration of Dox. The subsequent tissue was used for total RNA extraction.


title: PrP-null KO 0 days post-Dox 2

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: PrP-null KO 0 days post-Dox 2 DS

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: O days post Dox


title: PrP-null KO 0 days post-Dox 3 DS


title: TA female 66_SSA female 70

city: Adelaide

first: maria

last: caruso

state: SA

address: Frome Road

country: Australia

institute: SA Pathology

hyb_protocol: Labeled cDNA was hybridized to microarray slides printed with the CompuGen Human OligoLibrary (Compugen Human Oligo Library (v1) containing 18861 60-mer oligonucleotides, representing approximately 16,000 unique genes) by the Adelaide Microarray Centre (Australia).see the Adelaide Microarray Facility website

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments) twice at slightly different PMT voltage.

data_processing: Data analysis was performed in R (www.r-project.org) using the Limma package of Bioconductor (Gentleman, Carey et al. 2004; Smyth 2004). Loess print tip method was used to correct for dye-bias and intensity within each group of adjacent spots printed by one pin (Yang, Dudoit et al. 2002). Linear modelling was performed with the Limma package of Bioconductor (Smyth 2004).

organism: Homo sapiens

source_name: Sessile serrated adenoma

label_protocol: cDNA was labeled with Cy5 or Cy3 dyes using the Cy-Scribe post-labeling kit (Amersham) as per the instructions.

extract_protocol: Total cellular RNA was harvested with Trizol (Invitrogen, Carlsbad, CA) and further purified with the RNeasy RNA purification kit (Qiagen, Valencia, CA) according to the manufacturers instructions. cDNA was generated using 25-40 ug total RNA as a template and primed with PolyT(V)N (4.0 ug) and random hexamers (1.0 ug, Amersham, UK).

tag: Polyp type

value: SSA Gender:Female Age:70

source_name: Conventional polyp

value: TA Gender:Female Age:66


title: SSA female 69_TA female 73

value: TA Gender:Female Age:73

value: SSA Gender:Female Age:69


title: PrP overexpression HQK-3 0 days post-Dox DS

treatment_protocol: WT mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 following administration of Dox. The subsequent tissue was used for total RNA extraction.


title: TA female 73_SSA female 73

value: SSA Gender:Female Age:73


title: TA male 86_SSA male 68

value: SSA Gender:Male Age:68

value: TA Gender:Male Age:68


title: Spleen diet reverse

city: Barcelona

first: Joan

middle: C

last: Balasch

address: UAB Bellaterra faculty of Biosciences

department: Dpt. Cell Biology, Physiology and Immunology

country: Spain

institute: Universitat Autonoma Barcelona

description: To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes.

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, immunodiet and control diet cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. All samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning was performed with Axon scanner 4000B and images were processed with GenePix Pro 6.0.The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: After subtraction of mean background, locally weighted non-linear regression (Lowess) normalization was performed separately for each slide.

organism: Oncorhynchus mykiss

source_name: Diet D spleen (control fed)

label_protocol: cDNA Cy5 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: TriReagent manufacturer's protocol. RNA was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions.The RNA was stored at -80 ºC in ethanol 70% until use.

tag: RNA from spleen (control diet D)

source_name: Diet Q spleen (immunostimulant fed)

label_protocol: cDNA Cy3 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

tag: RNA from spleen (immunostimulant diet Q)


title: PrP overexpression HQK-2 0 days post-Dox


title: PrP-null KO 0 days post-Dox 3


title: TA male 74_SSA male 83

value: TA Gender:Male Age:83

value: SSA Gender:Male Age:74


title: PrP overexpression HQK-2 0 days post-Dox DS

treatment_protocol: Tg(HQK) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 following administration of Dox. The subsequent tissue was used for total RNA extraction.

value: 0 days after Dox admin

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 0 following administration of Dox. The subsequent tissue was used for total RNA extraction.

value: Wild-Type


title: SSA female 80_TA male 64

value: TA Gender:Male Age:64

value: SSA Gender:Female Age:80


title: Spleen diet direct

source_name: Diet D intestine (control fed)


title: Head Kidney (HK) diet direct

source_name: Diet Q HK (immunostimulant fed)

tag: RNA from HK (immunostimulant diet Q)

source_name: Diet D HK (control fed)

tag: RNA from HK (control diet D)


title: SSA female 87_TA female 75

value: TA Gender:Female Age:75

value: SSA Gender:Female Age:87


title: Head Kidney (HK) diet reverse

source_name: Diet Q intestine (control fed)


title: SSA_Ref_female_58

value: SSA Gender:Female Age:58

source_name: pooled normal colonic tissue

tag: pooled normal colonic tissue


title: SSA male 78_TA male 76

value: TA Gender:Male Age:78

value: SSA Gender:Male Age:78


title: Ref_SSA_female_83

value: SSA Gender:Female Age:83


title: TA female 68_SSA female 76

value: SSA Gender:Female Age:76

value: TA Gender:Female Age:68


title: Ref_SSA_female_58


title: Ref_SSA_female_76


title: SSA_Ref_female_87


title: Ref_SSA_female_87


title: genomic V4-L1-04

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

description:
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the
membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters
were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked
with a Geiger counter or re-scanned with a Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. New macroarrays were pre-treated for 30 min at 80ºC with 0.5% SDS to remove particles deposited during array printing. This step was not necessary in subsequent hybridizations. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X106dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1at 65ºC for 20 min in 2SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2SSC, 0.1% SDS. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantitation background substracted

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast genomic DNA

label_protocol:
Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 ul distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 uCi [–33P] dCTP (2500 Ci/mmol).
The mixture was incubated at 37C for 1–2 h. In order to eliminate non-incorporated components, Probe Quant G–50 columns (Amersham Biosciences) were used.

extract_protocol:
Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by
Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for
transformation of Escherichia coli. Gene 57:267–272

tag: V4-L1-04 filter hybridization with labeled yeast genomic (S288c) DNA. DNA labelling by random priming procedure and 33P-dCTP.


title: SSA_Ref_male_77

value: SSA Gender:Male Age:77


title: Ref_TA_male_64 (np.296.8)


title: Ref_TA_male_64


title: genomic V4-L1-03

tag: V4-L1-03 filter hybridization with labeled yeast genomic (S288c) DNA. DNA labelling by random priming procedure and 33P-dCTP.


title: genomic V4-L1-02

tag: V4-L1-02 filter hybridization with labeled yeast genomic (S288c) DNA. DNA labelling by random priming procedure and 33P-dCTP.


title: SSA_Ref_female_83


title: src1 mutant replicate 3

source_name: src1 mutant replicate 3 growing in exponential phase

label_protocol:
Yeast cDNA was labeled by reverse transcription. The reaction mixture consisted of 30 ug total RNA, 0.5 ug oligo(dT) (5´-T15VN-3´), 1 ul RNAse OUT (Invitrogen), and RNA-treated water were added to a microcentrifuge tube in a total volume of 10 ul. The mixture was incubated at 70ºC for 10 min and chilled on ice for 5 min.
Five ul of 5first-strand buffer, 3 ul 0.1M DDT, 1.5 ul dNTP mix (dATP, dGTP, dTTP 16 mM each, and dCTP 100  uM), 5 ul 33P–dCTP (10  uCi/ ul) and 1 ul SuperScript II RT (200 U/ ul, Invitrogen) were added in a final volume of 30 ul. The mixture was incubated at 43ºC for 1 h and the reaction stopped by adding 1 ul 0.5 M EDTA. Unincorporated nucleotides were removed by using MicroSpin S-300 HR columns (Amersham Bioscience) following the manufacturer’s instructions.

extract_protocol:
Total RNA from yeast cells was prepared as described by
Sherman et al. [1986], but using a multiple-sample automated
device (Fast-Prep, BIO101) to break the cells.
Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics.
Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

tag: Total RNA from src1 mutant yeast strain (BY4741, YML034w::kanMX4) growing in exponential phase in YPD


title: SSA_Ref_female_76


title: TA_Ref_female 82

value: TA Gender:Female Age:82


title: TA_Ref_male_64


title: Ref_SSA_male_77


title: Clear cell renal cell carcinoma 9: metastasis ccRCC-primary ccRCC

city: Shanghai

first: Guangwen

last: Cao

state: Shanghai

address: No.800,Xiangyin Road

department: Department of Epidemiology,Faculty of Health Service

country: China

institute: Second Military Medical University

description: Biological replicate 9 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42C  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50C), 0.1 SSC/0.2%SDS(50C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: VALUEs represent LOWESS normalized, background subtracted log2 (Metastasis/Primary) ratios.

source_name: Metastasis ccRCC

label_protocol: 2 ug of total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent). cDNAs were amplified at 40C for 2 hours in the presence of T7 RNA Polymerase(Agilent) and 4ul 25mM aaUTP(Ambion).Generated cRNA was purified with RNeasy mini Kit(QIAGEN).Mix 4ug amino allyl-modified cRNA and 100mg Cy3 NHS ester, incubate in the dark at room temperature(~25C) for 1 hour then purified with RNeasy mini Kit(QIAGEN).

growth_protocol: Fresh ccRCC tissues were immediately immersed in cold RPMI 1640 medium (GIBCO, Invitrogen Co., Grand Island, N.Y. ) containing 1% penicillin / streptomycin (GIBCO), 0.5% glutamine (GIBCO) and kept at 4°C for 30 min. Following removal of the surrounding fat, blood vessels, necrotic tissues, tumor tissue was mechanically minced with scissors in a sterile manner. Dissociated tumor cells were washed twice with PBS, and then resuspended in RPMI 1640 (Life Technologies, Inc., Grand Island, NY) supplemented with 20% fetal bovine serum (GIBCO), 2 mmol/L L-glutamine, 100 units/mL penicillin and 100 μg/ml streptomycin, and incubated at 37°C, 5% CO2, 95% humidity. The cells remained in culture until sufficiently confluent for a first tissue culture passage. Aliquots of cells were cryopreserved in 90% FCS, 10% dimethyl sulfoxide (Sigma, Saint Louis Mo. USA) and stored in liquid nitrogen after 1-2 passages. Because a variation of phenotype can occur at higher passages,28-30 we selected the ccRCC cultures at the 4th passage for gene expression analysis.Primary cultures from the metastatic ccRCC lesions were paired with those from the primary ccRCC lesions from the age (≤2 years) and gender matched ccRCC patients without distant metastasis. The metastatic and non-metastatic ccRCC cells were cultured under identical conditions, changing media and being passaged simultaneously.

extract_protocol: Total RNA was isolated from primary cultures using Trizol RNA isolation reagent (Life Technologies, Inc.) according to the manufacturer’s specifications. The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California).

tag: Quality metric=28S to 18

tag: Gender

value: Man

tag: Ethnic background

value: Han

tag: Histology

value: clear cell renal cell carcinoma

tag: Second site

value: bone

tag: Marterial

value: primary cultures from tumor tissues

source_name: Primary ccRCC

growth_protocol: same as for channel 1

extract_protocol: same as for channel 1


title: wt replicate 3

source_name: wt replicate 3 growing in exponential phase

tag: Total RNA from wt yeast strain (BY4741) growing in exponential phase in YPD


title: wt replicate 2

source_name: wt replicate 2 growing in exponential phase


title: Clear cell renal cell carcinoma 3: metastasis ccRCC-primary ccRCC

description: Biological replicate 3 of 9. Clear cell renal cell carcinoma, metastasis and primary cells from tissues

hyb_protocol: mix  Cy3 probes and Cy5 probes together, then transfer the solution to a 0.2 ml PCR tube,Incubated in a hybridization chamber at 42C for 16-18 hours After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42C  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50C), 0.1 SSC/0.2%SDS(50C) and 0.1 SSC(room temperature) before scanning.

tag: Days from patient diagnosis to excison

value: 1 month

tag: Diagnosis made by

value: CT and pathology

tag: Presenting symptoms

value: no apparent symptoms


title: wt replicate 1

source_name: wt strain exponential growth in YPD

tag: Total RNA from wt strain yeast strain (BY4741) growing in YPD exponential phase at 0.5 OD


title: Gastric cancer 3: metastasis GC- matched primary GC

description: Biological replicate 3 of 3.  Gastric cancer tissue, metastasis and matched primary tumor tissue.

source_name: Metastasis  GC

value: gastric adenocarcinoma

value: liver

source_name: Matched GC

value: gastric carcinoma


title: Clear cell renal cell carcinoma 7: metastasis ccRCC-primary ccRCC

description: Biological replicate 7 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

tag: TriZol procedure

value: blood in urine

value: lymph node near abdominal aorta


title: src1 mutant replicate 1

source_name: src1 mutant replicate 1 growing in exponential phase

tag: Total RNA from src1 mutant yeast strain (By4741, YML034w::kanMX4) growing in exponential phase in YPD


title: Ref_TA_female_82

tag: pooled normal colonic tissue

source_name: Conventional polyp

tag: Polyp type


title: Clear cell renal cell carcinoma 4: metastasis ccRCC-primary ccRCC

description: Biological replicate 4 of 9. Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues


title: Clear cell renal cell carcinoma 6: metastasis ccRCC-primary ccRCC

description: Biological replicate 6 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

source_name: Metastasis  ccRCC

value: primary culture from tumor tissues

value: no signifacant symptoms


title: Gastric cancer 2: metastasis GC- matched primary GC

description: Biological replicate 2 of 3.  Gastric cancer tissue, metastasis and matched primary tumor tissue.

value: gastric adeniocarcinoma cancer

value: gastric adenocarcinoma cancer


title: src1 mutant replicate 2

source_name: src1 mutant replicate 2 growing in exponential phase


title: Eca_PMMculture_rep3

status: Public on Aug 26 2008

city: Dundee

first: Pete

last: Hedley

address: Invergowrie

department: Genetics

country: United Kingdom

institute: SCRI

hyb_protocol: Labeled cDNA was made up to a volume of 80 ul with distilled water and denatured by heating at 98°C for 3 min. The denatured cDNA was mixed with 25 ul of control target and 105 ul of 2x hybridization buffer (Agilent Technologies, Inc.), and hybridization was carried out for 17 h at 60°C. After hybridization, the arrays were washed at room temperature in the dark for 1 min each with wash solution I (6x SSPE [1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA, pH 7.7] 0.005% N-lauroylsarcosine), followed by wash solution II (0.06x SSPE, 0.005% N-lauroylsarcosine). Array were dried by centrifugation.

scan_protocol: Arrays were scanned using an ArrayWoRx Auto scanner (Applied Precision) with appropriate exposure settings for Cy3 (595 nm) and Cy5 (685 nm) at a 9.756 um resolution, generating separate TIFF images. Intensity data were acquired from images using SoftWoRx Tracker software (Applied Precision). Images were imported and aligned with clone position information (Agilent GAL file) using automated and manual grid alignment features. Median spot and individual median background (annulus setting) intensity values were extracted for each wavelength and imported into analysis software.

data_processing: Spot intensity data were imported into GeneSpring (v. 7.3.1, Agilent Technologies Inc.). Microarray data was transformed to account for the dye-swap and normalised using default settings (LOWESS algorithm). Ratio of mutant/wild type = VALUE. Unreliable data (signal-background < 50 in 50% replicates) was removed by filtering. Transcripts were considered to be significantly altered in abundance in the mutant if the mean normalised signal from their probes was increased or decreased by more than 2x in the mutant compared with the wild type, with a Student's t-test P value < 0.05 (the experiment contained four biological replicates).

organism: Pectobacterium carotovorum

source_name: Eca dsbA mutant

label_protocol: In a reverse transcription reaction, 3 ug of total RNA was labeled in a 45 ul labeling reaction with 10 ul of a combination of short oligonucleotide (11-mer) primers (100 ng/ml) (14), 1 ul of spike RNA mix, 1.8 ul of 25x amino allyldeoxynucleoside triphosphate (dNTP) mixture, 4.5 ul of dithiothreitol (0.1 M), and 2 ul of reverse transcriptase in reaction buffer (Superscript II; Invitrogen). Primers and RNA were heated to 70°C for 10 min and cooled on ice followed by incubation for 2 h at 42°C. To denature the remaining RNA, 15 ul of 1 M NaOH and 15 ul of 0.5MEDTA (pH 8.0) were added and incubated for 10 min at 65°C. The reaction was neutralized with 15 ul of 1 M HCl. Purification of cDNA was done as described by the supplier (QIAGEN, Hilden, Germany). The Cy dye ester was added to 10 ul of cDNA in amber tubes (QIAGEN, Hilden, Germany) in a total volume of 13 ul, containing 2.0 ul of 1 M sodium carbonate and 1.0 ul of the appropriate Cy dye (suspended in dimethyl sulfoxide) and incubated for 1 h at room temperature in the dark. To the labeled cDNA, 3.0 ul of 4.0 M hydroxylamine hydrochloride was added and incubation was extended for another 30 min in the dark. The labeled targets were combined and mixed with distilled water and further diluted with 500 ul of PB buffer (QIAGEN, Hilden, Germany) before application to a QIAGEN MiniElute column for purification. Finally, cDNA was eluted in 10 ul of elution buffer. The labeling efficiency was estimated with 1 ul of the cDNA using a NanoDrop ND-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Each strain grown to an OD600 of ~3.4 in PMM

extract_protocol: The bacterial cells were incubated for at least 30 min on ice with 1% (vol/vol) phenol (pH 4.3) and 20% (vol/vol) ethanol for stabilization of RNA. Total RNA was isolated using a QIAGEN RNeasy RNA isolation kit as described by the manufacturer (QIAGEN,Hilden, Germany). RNA was quantified using a NanoDrop ND-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and the quality was assessed on an Agilent Bioanalyzer 2100 electrophoresis system (Agilent Technologies Inc., Palo Alto, CA).

tag: Subspecies

value: atroseptica

tag: Type

value: dsbA mutant

tag: Culture

value: in vitro

tag: Media

value: PMM

tag: Temperature

tag: Sampling

source_name: Eca wild type

value: wild type


title: Eca_PMMculture_rep2


title: Clear cell renal cell carcinoma 5: metastasis ccRCC-primary ccRCC

description: Biological replicate 5 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

tag: Quality metric=28S to 18

tag: Gender

value: Man

tag: Second site

value: bone

tag: Histology

value: clear cell renal cell carcinoma

tag: Ethnic background

value: Han

value: 1 month

value: primary cultures from tumor tissues


title: Clear cell renal cell carcinoma 8: metastasis ccRCC-primary ccRCC

description: Biological replicate 8 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

value: Women

tag: Days from patient diagnosis to excison

tag: Presenting symptoms

value: blood in urine

tag: Diagnosis made by

value: CT and pathology

tag: Marterial

source_name: Primary  RCC

value: Woman


title: Clear cell renal cell carcinoma 2: metastasis ccRCC-primary ccRCC

description: Biological replicate 2 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

value: liver


title: Eca_PMMculture_rep4


title: ChIP on chip p300 (IP infected versus IP mock) at 24 hours post infection

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: Data extraction and analyses were carried out using the Agilent Feature Extraction software (version 9.1.3.1) and Chip Analytics software (version 1.2). Probe signals were extracted with the Agilent Feature extraction software, normalized with Lowess normalization using the Chip Analytics software

hyb_protocol: Hybridization onto the Human Promoter array (Agilent-G4489A), washing, and scanning were carried out according to the manufacturer's instructions

scan_protocol: The arrays were scanned using an Agilent DNA Microarray scanner.

data_processing: Each ChIP profile was normalized to generate mean value of zero and variance of one, since the assay accurately captures the relative enrichment of an IP across an array.

source_name: IP Infected IMR90 fibroblasts

label_protocol: 2 μg of amplified material were labeled with Cy3 or Cy5 (PerkinElmer) using the Bioprime Labeling Kit (Invitrogen). DNA was mixed with 35 µl of random priming solution (Invitrogen Bioprime Kit) to a final volume of 75 µl, boiled for 5 min and quickly cooled in an ice-water bath for 5 min. The labeling reaction was completed with 60U Klenow, dNTPs (0.12 mM dATP, dGTP and dTTP and 0.06 mM dCTP), 1.28 mM Cy3 and Cy5 for input and IP (or IP from mock and IP from dl1500-infected cells) respectively, and incubated for 3h at 37°C. The labeled DNA was purified using Qiagen Qiaquick PCR purification Kit and the incorporation was measured with Nanodrop.

extract_protocol: 2x107 IMR90 lung fibroblasts were grown on 10 cm dishes to confluence. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in low serum media (2%). At the indicated times post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate (corresponding to 5x106 cells) were used for immunoprecipitation with a given antibody (listed in table S1); 10 µl of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP and INP DNA were amplified using the WGA Kit (Sigma)

tag: IP Infected IMR90 fibroblasts

source_name: IP Mock-infected IMR90 fibroblasts

tag: IP Mock-infected IMR90 fibroblasts


title: ChIP on chip p300 (IP infected versus IP mock) at 6 hours post infection


title: ChIP on chip PCAF (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip p130 (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip H3K18 acetylation (IP infected versus IP mock) at 6 hours post infection


title: Gastric cancer 1: metastasis GC- matched primary GC

description: Biological replicate 1 of 3.  Gastric cancer tissue, metastasis and matched primary tumor tissue.

value: gastric adenocarcinoma cancer


title: ChIP on chip H3K18 acetylation in R2G virus (IP infected versus IP mock) at 24 hours post infection


title: Eca_PMMculture_rep1

tag: Subspecies

value: atroseptica


title: ChIP on chip p300 in R2G virus (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip p107 (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip H3K18 acetylation in deltaCR2 virus (IP infected versus IP mock) at 24 hours post infection

source_name: IP infected IMR90 fibroblasts

tag: IP infected IMR90 fibroblasts


title: Clear cell renal cell carcinoma 1: metastasis ccRCC-primary ccRCC

description: Biological replicate 1 of 9.  Metastasis vs non-metastasis, clear cell renal cell carcinoma, primary cultures from tumor tissues

source_name: Metastasis ccRCC


title: ChIP on chip histone H3K9 acetylation for r2g virus (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip histone H3K9 acetylation (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip histone H4K16 acetylation (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip R2G e1a (IP infected versus INP infected) at 24 hours post infection

source_name: INP Infected IMR90 fibroblasts

tag: INP Infected IMR90 fibroblasts


title: ChIP on chip histone H3K9 acetylation for deltaCR2 virus (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip H3K18 acetylation (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip deltaCR2 e1a (IP infected versus INP infected) at 6 hours post infection


title: ChIP on chip histone H3 (IP infected versus IP mock) at 24 hours post infection


title: PrP overexpression HQK-3 4 days post-Dox

description: Uninfected aged-matched mice used as control

treatment_protocol: Wild type (WT)  mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 4 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

tag: Line

value: Wild-type

tag: Treatment

value: 4 days post Dox admin

value: Transgenic HQK


title: Chip on chip e1a (IP infected vs INP infected) 12 h post infection

extract_protocol: 2x107 IMR90 lung fibroblasts were grown on 10 cm dishes to confluence. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in low serum media (2%). At the indicated times post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate (corresponding to 5x106 cells) were used for immunoprecipitation with a given antibody (listed in table S1); 10 µl of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP and INP DNA were amplified using the WGA Kit (Sigma).

source_name: INP infected IMR90 fibroblasts

tag: INP infected IMR90 fibroblasts


title: ChIP on chip deltaCR2 e1a (IP infected versus INP infected) at 24 hours post infection


title: ChIP on chip Rb (IP infected versus IP mock) at 24 hours post infection


title: ChIP on chip R2G e1a (IP infected versus INP infected) at 6 hours post infection


title: Chip on chip e1a (IP infected vs INP infected) 6 h post infection

extract_protocol: 2x107 IMR90 lung fibroblasts were grown on 10 cm dishes to confluence. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in low serum media (2%). At the indicated times post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate (corresponding to 5x106 cells) were used for immunoprecipitation with a given antibody (listed in table S1); 10 µl of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP and INP DNA were amplified using the WGA Kit (Sigma)(3).


title: Chip on chip e1a (IP infected vs INP infected) 24 h post infection


title: Chip on chip e1a (IP infected vs INP infected) 2 h post infection


title: PBMC treated with rPA20 (9 of 12)

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: biological replicate 9 of 12

hyb_protocol: Slides were hybridized overnight ~16 hrs at 60 degree celcius

scan_protocol: Images scanned using GenePix 4000B (Axon Instruments)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. These were statisctically analyzed to idnetify significantly regulated genes. Imagene 6.0 and GeneSpring GX 7.3.1 were used for data analysis

source_name: Human peripheral blood mononuclear cells

label_protocol: TSA labling  and Detection kit (PerkinElmer) according to the manufactures protocol

growth_protocol: PBMC were isolated from blood samples collected from healthy volunteers

extract_protocol: Total RNA isolated using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacture's intructions

treatment_protocol: PBMC were treated with recombinant PA20

tag: PBMC treated with rPA20

source_name: commercial reference RNA

tag: Internal reference


title: PBMC treated with rPA20 (10 of 12)

description: biological replicate 10 of 12


title: PBMC not treated with rPA20  (2 of 2)

description: biological replicate 2 of 3

tag: PBMC not treated with rPA20


title: PBMC treated with rPA20 (11 of 12)

description: biological replicate 11 of 12


title: PBMC treated with rPA20 (5 of 12)

description: biological replicate 5 of 12


title: PBMC treated with rPA20 (8 of 12)

description: biological replicate 8 of 12


title: PBMC treated with rPA20 (12 of 12)

description: biological replicate 12 of 12


title: PBMC treated with rPA20 (6 of 12)

description: biological replicate 6 of 12


title: PBMC treated with rPA20  (3 of 12)

description: biological replicate 3 of 12


title: PBMC treated with rPA20 (7 of 12)

description: biological replicate 7 of 12


title: PBMC treated with rPA20 (4 of 12)

description: biological replicate 4 of 12


title: Expression profile 24 hours post infection for deltaCR2 e1a mutant

hyb_protocol: Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol G4140-90050 v.5.7

scan_protocol: Agilent DNA Microarray Scanner

data_processing: Triplicate samples of 250 ng of RNA from three independent infections from dl1500- and mock-infected primary IMR90 fibroblasts cells were amplified and labeled with Cy5 and Cy3 (Perkin Elmer), respectively, using the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol according to manufacturer's instructions. Labeled RNA was hybridized to the Agilent Human whole-genome array (G2534-60011) and Expression data were extracted using Agilent Feature Extraction software (version 9.1.3.1). Raw data was natural log (ln) transformed and signals from multiple probes for the same gene were averaged. Each array was normalized so that the mean was zero and standard deviation was one. Data from three independent replicate experiments were averaged.

source_name: infected IMR90 fibroblasts total labeled RNA

extract_protocol: qiagen RNAeasy Kit for total RNA extraction. Sample has been extracted at 24 hours post infection

tag: infected IMR90 female fibroblasts total labeled RNA

source_name: Mock infected IMR90 fibroblasts

tag: Mock infected female IMR90 fibroblasts


title: PBMC treated with rPA20  (2 of 12)

description: biological replicate 2 of 12


title: Expression profile 12 hours post infection for dl1500 virus expressing WT small e1a

label_protocol: Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol G4140-90050 v.5.7

extract_protocol: qiagen RNAeasy Kit for total RNA extraction. Sample has been extrqacted at 6 hours post infection

tag: Mock infected IMR90 female fibroblasts total labeled RNA


title: Expression profile 24 hours post infection for dl1500 virus expressing WT small e1a

tag: Infected IMR90 female fibroblasts total RNA


title: Expression profile 24 hours post infection for R2G e1a mutant

source_name: infected IMR90 fibroblasts

tag: Mock infected IMR90 female fibroblasts


title: Chip on chip CBP (IP infected vs IP Mock) 24 h post infection

source_name: IP mock-infected IMR90 fibroblasts

tag: IP mock-infected IMR90 fibroblasts


title: Khd1 IP (2)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/30144.gif
Strain Name: tagged

scan_protocol: Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B [81971];  Scanning software = AxImageIO

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: tot. RNA Khd1 extract (2)

tag: tot. RNA Khd1 extract (2)

source_name: Khd1 IP RNA (2)

label_protocol: Gerber et al. (2004) PLoS Biology; The protocol can be found in the Series supplementary file

tag: Khd1 IP RNA (2)


title: Khd1 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29827.gif
Strain Name: tagged

source_name: total RNA Khd1 extract (1)

tag: total RNA Khd1 extract (1)

source_name: Khd1 IP RNA  (1)

tag: Khd1 IP RNA  (1)


title: BY4741 mock (1)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36816.gif
Strain Name: not tagged

source_name: BY4741 tot. RNA extract (1)

tag: BY4741 tot. RNA extract (1)


title: Expression profile 6 hours post infection for dl1500 virus expressing WT small e1a

source_name: Mock infection


title: BY4741 mock (4)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37362.gif
Strain Name: not tagged

source_name: BY4741 tot. RNA extract (4)

tag: BY4741 tot. RNA extract (4)


title: BY4741 mock (2)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36817.gif
Strain Name: not tagged

source_name: BY4741 tot. RNA extract (2)

tag: BY4741 tot. RNA extract (2)


title: PBMC not treated with rPA20  (1 of 2)

description: biological replicate 1 of 3


title: Khd1 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32102.gif
Strain Name: tagged

source_name: total RNA Khd1 extract (3)

tag: total RNA Khd1 extract (3)

source_name: Khd1 IP RNA (3)

tag: Khd1 IP RNA (3)


title: PBMC treated with rPA20  (1 of 12)

description: biological replicate 1 of 12

tag: PBMC treated with rPA20

tag: Internal reference


title: GCT-27X1

status: Public on Aug 25 2008

city: Kiel

first: Franz-Josef

last: Mueller

state: Schleswig-Holstein

address: Niemannsweg 147

country: Germany

institute: Zentrum für Integrative Psychiatrie

description:
1562259037C
germ cell tumor cell line undifferentiated

hyb_protocol: Sucessfully labeled cRNA samples were then hybridized to Human Ref-8 BeadChips and Human  WG6 BeadChips (Illumina) according to the manufacturer's instructions (approximately 23,000 identical gene probes are represented on both array designs), using equipment specified by the manufacturer (Illumina). Briefly, 850 ng biotin-labeled cRNA in 11.3 µl nuclease-free water was adjusted to 34 µl through the addition of 22.7 µl of 5:3 HybE1 buffer/formamide. The sample was heated at 65°C for 5 min, allowed to cool to room temperature, and then immediately added to a single array of an 8-array Human Ref-8 BeadChip. Once all 8 samples were added to each BeadChip, it was sealed in a Hyb Cartridge and incubated for 16 h at 55°C with rotation in an Illumina hybridization oven (rotation setting 5). Following overnight hybridization, BeadChips were moved to a slide rack and serially washed using gentle rotation in glass staining dishes filled with a) 250 ml Illumina Wash Buffer×5 min, b) 250 ml 100% ethanol×10 min, c) 250 ml Illumina Wash Buffer×2 min. BeadChips were then blocked for 10 min in 4 ml Block E1 buffer (Illumina), followed by staining for 10 min in 1 µg/ml Streptavidin-Cy3 conjugate (GE Healthcare) in Block E1 buffer. Stained BeadChips were finally washed using gentle rotation in a glass staining dish filled with 250 ml Illumina Wash Buffer×5 min. BeadChips were dried by centrifugation at 280×g for 4 min and stored in a light-tight box until reading.

scan_protocol: Processed arrays were read using a BeadStation array reader (Illumina) according to the manufacturer's instructions. Scan settings were for single color (green) scanning.

data_processing: All arrays (Human Ref-8 BeadChips and Human  WG6 BeadChips) were uploaded in BeadStudio version 1.5.1.3 and the intensity values for all 23,000 identical probes on both array designs were extracted; Normalization = none; Array Content = Human_RefSeq-8.xml; Error Model = none; uploaded into R/Bioconductor; Quantile normalized with R/package Affy

label: biotin

source_name: germ cell tumor cells

label_protocol: total RNA samples were quality assessed using Nanodrop Spectrophotometer, Invitrogen Qbit Spectrophotometer and the Agilent Bioanalyzer. Samples were then amplified one round, using an RNA Amplification Kit (Ambion) according to the manufacturer's instructions. The resulting purified cDNA product of was resuspended and dried down in a speedvac centifuge. cDNA was then converted to cRNA using an in vitro transcription kit according to the manufacturer's instructions (Roche),followed by another round of QC with Nanodrop/Bioanalyzer

growth_protocol: in vitro preparations were harvested, derived, differentiated and/or grown according to published protocols for the respective lines and samples. For further details and references please refer to Supplementary Tables 1 - 8 of the manuscript Regulatory networks define phenotypic classes of human stem cell lines

extract_protocol: Depending on the lab that suplied samples, different extraction methods were used according to standard/manufacturers protocols: TriZOL extraction, Quiagen Rneasy Mini Kit or Ambion Mirvana

tag: at pluripotent stage

value: YES

tag: Stem Cell Matrix

value: test dataset

tag: SCM core sNMF cluster


title: GCT-C4

description:
1562259037F
germ cell tumor cell line undifferentiated


title: hFib2-iPS5

description:
1562259037B
iPS cells from adult dermal fibroblasts

source_name: iPS cells


title: BG03-4

description:
1512391098F
CM for 32 passage (BG03)

source_name: ES cells_ undifferentiated


title: MSC-iPS1

description:
1562259037E
iPS cells from mesenchymal stem cells


title: Hu J6 P74-2

description:
1400401044C
embryonic stem cell line


title: BG03-3

description:
1512391098B
(S2)-StemPro SFM for 32 passage (BG02)


title: BG02-2

description:
1512391098E
CM for 64 passage (BG02)


title: Hu J3 p56-2

description:
1400401019E
embryonic stem cell line


title: Hu J6 P74-1

description:
1400401019D
embryonic stem cell line


title: ES2

description:
1521406075A
embryonic stem cell line


title: ES4

description:
1521406075E
embryonic stem cell line


title: ES3

description:
1521406075C
embryonic stem cell line


title: MSC-DMEM

description:
1521406075G
Bone marrow mesenchymal stem cells, cultured in standard MSC conditions (10 FBS, DMEM)

source_name: Mesenchymal Stem Cells

value: NO


title: BY4741 mock (3)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37361.gif
Strain Name: not tagged

source_name: BY4741 tot. RNA extract (3)

label_protocol: not provided

extract_protocol: not provided

tag: BY4741 tot. RNA extract (3)


title: GCT-72

description:
1562259037A
germ cell tumor cell line undifferentiated


title: Hu J3 p56-1

description:
1400364009F
embryonic stem cell line


title: Hu DM3 P12 (CyT203)

description:
1400401044E
embryonic stem cell line


title: 2102Ep P85-2

description:
1400401044A
Teratocarcinoma cell line 2102ep undifferentiated

source_name: Teratocarcinoma cells


title: BG02-1

description:
1512391098A
(S1)-StemPro SFM for 10 passage (BG02)


title: Ntera2 P9-2

description:
1400401044B
NTera2 (human embryonic carcinoma stem cells) undifferentiated


title: Hu Cyt25 P12  (CyT25)

description:
1400401044D
embryonic stem cell line


title: HUES20

description:
1400401043E
embryonic stem cell line


title: HUES22

description:
1400401043G
embryonic stem cell line


title: MSC-MesenPRO

description:
1521406075H
Bone marrow mesenchymal stem cells, cultured in Invitrogen MesenPro reduced serum formulation


title: Hu MSC donor1 P10

description:
1400401044H
Bone marrow mesenchymal stem cells


title: Ntera2 P9-1

description:
1400401043B
NTera2 (human embryonic carcinoma stem cells) undifferentiated


title: HUES21

description:
1400401043F
embryonic stem cell line


title: Hu MSC donor2 P8

description:
1400401043H
Bone marrow mesenchymal stem cells


title: BG01V P29

description:
1400401043C
embryonic stem cell line, genetic variant of BG01


title: HUES9

description:
1400401043D
embryonic stem cell line


title: WA01-1

description:
1562259005A
embryonic stem cell line


title: Huevec BF4

description:
1565311056B
human umbilical vein endothelial cells

source_name: human umbilical vein endothelial cells


title: HFB2050-4

description:
1562259005F
long term cultured fetal neural progenitor line, 13 week old fetus

source_name: Fetal neural stem cell line


title: SC11-1

description:
1562259005C
postmortem derived astrocytes

source_name: Astrocytes, primary


title: HSF6-2

description:
1565311056F
embryonic stem cell line


title: HSF6-1

description:
1565311056E
embryonic stem cell line


title: Huevec WF2

description:
1565311056D
human umbilical vein endothelial cells


title: HFB2050-3

description:
1562259005E
long term cultured fetal neural progenitor line, 13 week old fetus


title: BJ1-iPS12

description:
1562259037D
iPS cells from neonatal foreskin fibroblasts


title: WA01-2

description:
1562259005B
embryonic stem cell line


title: WA09-11

description:
1488802023F
embryonic stem cell line-isolated colonies


title: Huevec BF2

description:
1565311056A
human umbilical vein endothelial cells


title: Huevec WF1

description:
1565311056C
human umbilical vein endothelial cells


title: WA09-10

description:
1488802023E
embryonic stem cell line-isolated colonies


title: HFT13 P32-2

description:
1565311035E
Korean equiv to 2050_ from Kook in Park


title: SC11-2

description:
1562259005D
postmortem derived astrocytes


title: HFT13 p47-2

description:
1565311035D
Korean equiv to 2050_ from Kook in Park


title: 2102Ep P85-1

description:
1400401043A
Teratocarcinoma cell line 2102ep undifferentiate


title: HS27Fib-5

description:
1565311020F
male foreskin fibroblasts

source_name: Feeder _ Fibroblasts


title: HFT13 P32-1

description:
1565311025B
Korean equiv to 2050_ from Kook in Park


title: SM3-1

description:
1565311025A
fetal NPC (16th week), Neurospheres

source_name: Primary fetal neural progenitors


title: HFT13 p40-2

description:
1565311035A
Korean equiv to 2050_ from Kook in Park


title: HFT13 P40-1

description:
1565311025D
Korean equiv to 2050_ from Kook in Park


title: SM3-2

description:
1565311035C
fetal NPC (16th week), Neurospheres


title: WA09-9

description:
1565311020E
embryonic stem cell line-isolated colonies


title: HS27Fib-4

description:
1565311020D
male foreskin fibroblasts


title: HFT13 p47-1

description:
1565311025F
Korean equiv to 2050_ from Kook in Park


title: WA09-7

description:
1565311003E
embryonic stem cell line-isolated colonies


title: HUVEC Cauc

description:
1565311020C
Human Umbilical Vein Endothelial Cells

source_name: Human Umbilical Vein Endothelial Cells


title: HS27Fib-3

description:
1565311003F
male foreskin fibroblasts


title: WA09-8

description:
1565311020B
embryonic stem cell line-isolated colonies


title: PEL P9

description:
1565311020A
primitive endodermal line from ESC_unpublished_method

source_name: Feeder _ hESC_derived


title: HUVEC

description:
1565311003A
Human Umbilical Vein Endothelial Cells


title: PEL-4

description:
1565311003D
primitive endodermal line from ESC_unpublished_method


title: PEL-3

description:
1565311003B
primitive endodermal line from ESC_unpublished_method


title: SC33BFib

description:
1401771144C
fibroblasts from postmortem skin biopsies

value: core dataset


title: WA09 P50

description:
1565311003C
embryonic stem cell line-isolated colonies


title: SC33AFib

description:
1401771143A
fibroblasts from postmortem skin biopsies


title: SC30AFib

description:
1401771141E
fibroblasts from postmortem skin biopsies


title: HS27Fib-1

description:
1351945015B
male foreskin fibroblasts


title: HS27Fib-2

description:
1351945015A
male foreskin fibroblasts


title: SC30BFib

description:
1546515010E
fibroblasts from postmortem skin biopsies


title: SC31AMSC

description:
1401771141F
Bone marrow mesenchymal stem cells, CD105+, CD34-


title: SC31BMSC

description:
1546515010F
Bone marrow mesenchymal stem cells, CD105+, CD34-


title: SC41BMSC

description:
1401771144D
Bone marrow mesenchymal stem cells, CD105+, CD34-


title: SC01AGlia

description:
1401771141C
postmortem derived astrocytes


title: SC01BGlia

description:
1546515010C
postmortem derived astrocytes


title: SC41AMSC

description:
1401771143B
Bone marrow mesenchymal stem cells, CD105+, CD34-


title: BMSC21

description:
1400364009A
Bone marrow mesenchymal stromal cells


title: BMSC25

description:
1400364009B
Bone marrow mesenchymal stromal cells


title: ASTRO-2

description:
1412091135E
astrocytes derived from neurosurgical specimens


title: SC23ANPC

description:
1401771141D
postmortem neural progenitors, monolayer

source_name: Postmortem neural precursors


title: SC23BNPC

description:
1546515010D
postmortem neural progenitors, monolayer


title: ASTRO-1

description:
1412091138C
astrocytes derived from neurosurgical specimens


title: SC30NSph-2

description:
1412091138B
postmortem neural progenitors spheres


title: HANSE 8-2

description:
1401771144F
surgery derived neural progenitor cells

source_name: Surgery derived neural progenitor


title: SC30ML-1

description:
1412091135C
postmortem neural progenitors, monolayer


title: SC30NSph-1

description:
1412091135A
postmortem neural progenitors, spheres


title: HANSE 5 A-2

description:
1383656043C
surgery derived neural progenitor cells (technical replicate)


title: HANSE 6 H-1

description:
1412091135D
surgery derived neural progenitor cells


title: HANSE 5 C-1

description:
1383656034D
surgery derived neural progenitor cells


title: HANSE 5 H-1

description:
1383656035E
surgery derived neural progenitor cells


title: HANSE 6 H-2

description:
1412091138F
surgery derived neural progenitor cells


title: HANSE 8-1

description:
1401771143D
surgery derived neural progenitor cells


title: HANSE 5 H-3

description:
1412091135F
surgery derived neural progenitor cells


title: SC30ML-2

description:
1412091138E
postmortem neural progenitors, monolayer


title: HANSE 5 H-2

description:
1383656043A
surgery derived neural progenitor cells (technical replicate)


title: HANSE 4 A-1

description:
1383656037F
surgery derived neural progenitor cells


title: HANSE 5 C-2

description:
1383656035C
surgery derived neural progenitor cells (technical replicate)


title: HANSE 5 A-1

description:
1383656034C
surgery derived neural progenitor cells


title: HANSE 4 HCA-1

description:
1383656034B
surgery derived neural progenitor cells


title: HANSE 3 H-1

description:
1383656034E
surgery derived neural progenitor cells


title: HANSE 4 A-2

description:
1383656035B
surgery derived neural progenitor cells (technical replicate)


title: HANSE 3 A-2

description:
1383656051B
surgery derived neural progenitor cells (technical replicate)


title: HANSE 4 HCA-2

description:
1383656043F
surgery derived neural progenitor cells (technical replicate)


title: HANSE 4 HDG-1

description:
1383656043B
surgery derived neural progenitor cells


title: HANSE 4 HDG-2

description:
1383656051D
surgery derived neural progenitor cells (technical replicate)


title: HANSE 3 A-1

description:
1383656043E
surgery derived neural progenitor cells


title: HANSE 4 C-1

description:
1383656043D
surgery derived neural progenitor cells


title: HANSE 4 C-2

description:
1383656051F
surgery derived neural progenitor cells (technical replicate)


title: HANSE 3 H-2

description:
1383656051C
surgery derived neural progenitor cells (technical replicate)


title: HANSE 2 C-1

description:
1383656037E
surgery derived neural progenitor cells


title: HANSE 2 H-2

description:
1383656051E
surgery derived neural progenitor cells (technical replicate)


title: HANSE 2 C-2

description:
1383656035F
surgery derived neural progenitor cells (technical replicate)


title: HOPC-2

description:
1334328026C
A2B5 positive NCAM negative human fetal cells (technical replicate)

source_name: Fetal glial restricted progenitors


title: HANSE 1 C-1

description:
1383656037A
surgery derived neural progenitor cells


title: HANSE 2 H-1

description:
1383656037B
surgery derived neural progenitor cells


title: HANSE 1 C-2

description:
1383656034F
surgery derived neural progenitor cells (technical replicate)


title: HANSE 1 A-1

description:
1383656034A
surgery derived neural progenitor cells


title: HANSE 1 A-2

description:
1383656035D
surgery derived neural progenitor cells (technical replicate)


title: hAPC-3

description:
1400401019A
CD44_ positive human fetal progenitors (technical replicate)

source_name: Astrocyte precursors


title: hAPC-2

description:
1334328023C
CD44_ positive human fetal progenitors (technical replicate)


title: HOPC-1

description:
1334328027F
A2B5 positive NCAM negative human fetal cells


title: HANSE 1 H-1

description:
1383656037D
surgery derived neural progenitor cells


title: SM2-2

description:
1546515010B
fetal NPC (16th week), Neurospheres


title: HANSE 1 H-2

description:
1383656035A
surgery derived neural progenitor cells (technical replicate)


title: HNSCHIP-2

description:
1334328025C
Neural stem cells, fetal, hippocampal, Neurospheres (technical replicate)


title: SM1-2

description:
1412091138D
fetal NPC (18th week), Neurospheres


title: hAPC-1

description:
1334328022D
CD44_ positive human fetal progenitors


title: HFB2050-1

description:
1323961026C
long term cultured fetal neural progenitor line, 13 week old fetus


title: HNSCCTX-2

description:
1334328025E
Neural stem cells, fetal, cortical, Neurospheres (technical replicate)


title: HFT13-1

description:
1412091146E
Korean equiv to 2050_ from Kook in Park


title: HFT13-2

description:
1412091145E
Korean equiv to 2050_ from Kook in Park


title: SM2-1

description:
1401771141B
fetal NPC (16th week), Neurospheres


title: THD-hFB17

description:
1400364009D
5_2003 (12 week fetus) used in methylation study


title: THD-hWB15

description:
1400364009C
5_2003 (14 week fetus) used in methylation study


title: NT2 PA6-6

description:
1334328007C
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells

source_name: Teratocarcinoma-differentiated


title: HNSCHIP-1

description:
1334328026E
Neural stem cells, fetal, hippocampal, Neurospheres


title: NT2 CM-8

description:
1334310004D
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 PA6-5

description:
1334310004F
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: HNSCCTX-1

description:
1334328027C
Neural stem cells, fetal, cortical, Neurospheres


title: NT2-3

description:
1351945004A
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: SM1-1

description:
1412091135B
fetal NPC (18th week), Neurospheres


title: HFB2050-2

description:
1323961026D
long term cultured fetal neural progenitor line, 13 week old fetus


title: NT2 CM-6

description:
1334328026F
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 CM-7

description:
1334328007B
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2-1

description:
1351945004D
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 CM-3

description:
1334310004E
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2-2

description:
1334328007D
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 CM-4

description:
1351945004E
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: MIZ5D-2

description:
1412091146C
Mizmedi line 5, a male line made in 2003

source_name: Embryoid bodies


title: NT2 PA6-2

description:
1334328025F
NTera2 (human embryonic carcinoma stem cells), Flow Cytometry selected by p75 and grown for 2 weeks on PA6 cells (mouse stromal cell line)


title: NT2 CM-2

description:
1351945004F
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: MIZ6D-2

description:
1412091145D
Mizmedi line 6


title: PEL-1

description:
1334328025D
primitive endodermal line from ESC_unpublished_method


title: MIZ6D-1

description:
1412091146A
Mizmedi line 6


title: R-ES-NSC-5

description:
1400364008E
ES cells_ differentiated by shin_unpublished method

source_name: ES_differentiated neural stem cells


title: NT2 CM-5

description:
1334328027B
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 PA6-1

description:
1334328027D
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: MIZ4D-1

description:
1473301122F
Mizmedi line 4


title: NT2 PA6-4

description:
1351945004B
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: NT2 PA6-3

description:
1334328007F
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: MIZ5D-1

description:
1473301122B
Mizmedi line 5, a male line made in 2003


title: R-ES-NSC-3

description:
1400364008C
ES cells_ differentiated by shin_ unpublished method


title: MIZ4D-2

description:
1412091145B
Mizmedi line 4


title: 2102Ep

description:
1400364009E
Teratocarcinoma cell line 2102ep


title: PEL-2

description:
1334328026B
primitive endodermal line from ESC_unpublished_method


title: R-ES-NSC-2

description:
1400364008B
NSC derived from BG02 acc to method in Shin et al 2006


title: SNU16NS-2

description:
1351945015D
ES_derived neural stem cells_ JPL_Moon_collab_unpublished method


title: NT2 CM-1

description:
1334310004B
NTera2 (human embryonic carcinoma stem cells) differentiated to dopaminergic neuronal like cells


title: R-ES-NSC-1

description:
1400364008A
NSC derived from BG02 acc to method in Shin et al 2006


title: ESC_NSC_N8-2

description:
1334328025B
ES_dervied Neural stem cells (technical replicate)


title: R-ES-NSC-4

description:
1400364008D
ES cells_ differentiated by shin_unpublished method


title: ESC_NSC_N8-1

description:
1334328026A
ES_derived Neural stem cells


title: SNU16NS-1

description:
1351945015C
ES_derived neural stem cells_ JPL_Moon_collab_unpublished method


title: ESC_NSC_N7-2

description:
1334328027A
ES_dervied Neural stem cells (technical replicate)


title: ESC_NSC_N7-1

description:
1334328025A
ES_dervied Neural stem cells


title: ESC_NSC_N6-2

description:
1334328021F
ES_dervied Neural stem cells (technical replicate)


title: ESC_NSC_N6-1

description:
1334328023B
ES_dervied Neural stem cells


title: ESC_NSC_N9-1

description:
1334328022E
ES_dervied Neural stem cells


title: NSWA09-4-2

description:
1401771144E
Neural stem cells from hES WA09_ RG__unpublished method


title: ESC_NSC_N9-2

description:
1334328023E
ES_dervied Neural stem cells (technical replicate)


title: NSWA09-2-2

description:
1323961026B
Neural stem cells from hES WA09_ RG__unpublished method


title: NSWA09-1-2

description:
1334328022C
WA09 cells from BIMR_unpublished method


title: NSWA09-1-1

description:
1334328021C
WA09 cells from BIMR_unpublished method


title: NSWA09-4-1

description:
1401771143C
Neural stem cells from hES WA09_ RG__unpublished method


title: NSWA09-2-1

description:
1323961026A
Neural stem cells from hES WA09_ RG__unpublished method


title: ESC_NSC_N1-1

description:
1334328021E
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG1)


title: ESC_NSC_N3-2

description:
1334328021D
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG3, technical replicate)


title: ESC_NSC_N2-1

description:
1334328022A
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG2)


title: NSWA09-1-3

description:
1351945004C
WA09 cells from BIMR_unpublished method


title: ESC_NSC_N5-2

description:
1334328022B
NSC derived from I6 acc to method in Shin et al 2006 (NSC I6p28, technical replicate)


title: ESC_NSC_N1-2

description:
1334328023F
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG1, technical replicate)


title: ESC_NSC_N5-1

description:
1334328021B
NSC derived from I6 acc to method in Shin et al 2006 (NSC I6p28)


title: ESC_NSC_N5-3

description:
1400401019H
NSC derived from I6 acc to method in Shin et al 2006


title: ESC_NSC_N4-2

description:
1334328022F
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG4, technical replicate)


title: ESC_NSC_N3-1

description:
1334328023A
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG3)


title: Hues7-1

description:
1546515010A
embryonic stem cell line

source_name: ES cells_ undifferentiated


title: Hues13-2

description:
1401771144B
embryonic stem cell line


title: ESC_NSC_N2-2

description:
1334328023D
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG2, technical replicate)


title: ESC_NSC_N4-1

description:
1334328021A
Noggin_treated hES acc to method in Itsykson et al 2005 (Pera, Reubinoff)_HES1 (NOG4)


title: Hues13-1

description:
1401771144A
embryonic stem cell line


title: Miz5-2

description:
1412091146F
Mizmedi line 5, a male line made in 2003


title: H2O2 30 min B

city: Albuquerque

first: Anthony

last: Aragon

state: NM

address: Castetter Hall Room 214

institute: University of New Mexico

description: Reference sample RNA consisted of a mixture of RNA from worms, following recovery, that were exposed to 37°C for 3.5 hours, 42°C for 3.5 hours, PAMPs (50ug/ml peptidoglycan: LPS: laminarin) for 6.0 hours, and PZQ (40ug/ml) for 0.5 hours at 37°C.

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40% formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for three hours at 42°C in hybridization buffer prior to hybridization with labeled probes.  Labeled cDNA was hybridized overnight at 42°C, to 7,066 S. japonicum and 12,166 Schistosoma mansoni element oligonucleotide arrays purchased from Agilent Technologies and described by Gobert and colleagues. Only the Schistosoma mansoni elements were considered in the analyses.

scan_protocol: Microarray slides were scanned using a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues [26]. A preloaded Schistosoma mansoni grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians.

data_processing: Microarray analysis was performed using samples derived from the 0 (untreated), 30, 60 and 240 min time points from both stress experiments. Raw expression data for each element was expressed as a ratio of the treatment (Cy5) to the common reference sample (Cy3). Expression ratios obtained for genes with the untreated samples were then subtracted from all sample ratios. Transcripts expressed ±1.0 log2, in both biological replicates, in either the 30 and 60 min, 60 and 240 min or 30, 60 and 240 min samples after this subtraction step were considered to be differentially expressed. Unsupervised hierarchical clustering analyses were performed on all microarrays.

organism: Schistosoma mansoni

source_name: Adult Schistosoma mansoni

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µl 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5 x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Schistosome infected mice and snails were supplied by Dr. Fred A. Lewis, NIAID Schistosomiasis Resource Center at the Biomedical Research Institute (Rockville, MD), through NIAID contract NO1-A1-30026. The abdomens of female SW mice were exposed to 125 Schistosoma mansoni PR-1 cercaria. Six weeks post exposure, mice were anesthetized and worms harvested by cardiac perfusion with enriched RPMI media (RPMI 1640 containing 20% fetal calf serum, 10,000 IU Penicillin, 10 mg/ml Streptomycin). Mice were subsequently euthanized by cervical dislocation. All animal experimentation complied with the policies, regulations and guidelines mandated by the Institutional Animal Care and Use Committee, University of New Mexico. Prior to all experiments, adult worms were allowed to recover overnight in enriched RPMI media at 37°C. This and all subsequent procedures that required worms to be maintained at 37 or 42°C (see below) were performed using a water jacketed incubator with 5% CO2.

extract_protocol: RNA was isolated from thawed worms using an RNeasy® Mini kit (Qiagen) according to the manufacturer’s instructions, eluted with 30 µl of RNase free distilled water (dH2O) and quantified using a NanoDrop® ND-1000 spectrophotometer using ND-1000 3.3 software (NanoDrop Technologies). RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip® Kit (Agilent Technologies).

treatment_protocol: Individual groups of 12 male and 12 female worms were placed into six Petri dishes containing 5 mL enriched RPMI media pre-warmed to 37°C. Oxidative stress was induced in schistosomes using H2O2. Individual groups of 12 male and 12 female worms were each placed into Petri dish containing 5 mL enriched RPMI media and H2O2 added to a final concentration of 100 µM. Worms were then incubated at 37°C and harvested after 0 (prior to the addition of H2O2),  30, 60, and 240 min as described above.

tag: Adult Schistosoma mansoni PR1 strain

tag: Adult Schistosoma mansoni PR1 strain common reference


title: Hues7-2

description:
1401771141A
embryonic stem cell line


title: H2O2 0 min B


title: BG01

description:
1400401019G
embryonic stem cell line


title: H2O2 240 min B


title: H2O2 60 min A


title: Miz5-1

description:
1473301122A
Mizmedi line 5, a male line made in 2003


title: H2O2 60 min B


title: hES1

description:
1400364008H
Relicell embryonic stem cell line_ used in methylation study


title: Miz6-2

description:
1412091146B
Mizmedi line 6


title: H2O2 0 min A


title: Miz6-1

description:
1473301122C
Mizmedi line 6


title: Miz4-1

description:
1473301122D
Mizmedi line 4


title: H2O2 240 min A


title: H2O2 30 min A


title: Miz4-2

description:
1412091145A
Mizmedi line 4


title: Heat shock 240 min A

treatment_protocol: Individual groups of 12 male and 12 female worms were placed into six Petri dishes containing 5 mL enriched RPMI media pre-warmed to 37°C. One dish was immediately harvested (0 h sample) by replacing the media with 600 µL of RLT buffer (Qiagen) containing 1 % β-ME (RLT/β-ME buffer) and homogenizing the worms (Kontes Glass Company). The homogenate was then frozen at -80°C until RNA was extracted as described below. The media in the remaining 5 dishes was replaced by 5 mL enriched RPMI media pre-warmed to 42°C and the dishes incubated at 42°C. Worms were then harvested as described above after 30, 60, and 240 min. A control group of 12 male and 12 female worms in 5 mL enriched RPMI media was maintained at 37°C and harvested after 4.0 h.


title: Heat shock 0 min B


title: Heat shock 240 min B


title: Heat shock 30 min A


title: Heat shock 30 min B


title: BG03-2

description:
1400364008G
embryonic stem cell line


title: WA09-6

description:
1351945015F
embryonic stem cell line


title: Heat shock 60 min A


title: Liver_TCPOBOP_CAR/PXR_rep3

status: Public on Aug 23 2008

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: Sterolgene V1 slides were washed before hybridization at room temperature 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. Samples were denatured and hybridized in 3xSSC and 0.2% SDS hybridization buffer at 65˚C for 16 hours using humidified hybridization chambers (HybChambers, GeneMachines). After hybridizations slides were washed at room temperature for 5 min in 2xSSC and 0.5% SDS, followed by 5 min in 0.5xSSC, then 5 min in 0.05xSSC and dried by centrifugation.

scan_protocol: Slides were scanned with Affimetrix 428 Array Scanner using Software Jaguar 2.0. Images were analyzed Gene Pix Pro 6.0 (Molecular Devices Corporation). The median feature and local background intensities were extracted together with the estimates of their standard deviation.

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs and housekeeping controls. Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples.

source_name: Liver, TCPOBOP-treated

label_protocol: Firefly luciferase (Promega) was added as an universal reference for microarray experiment. 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol.

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were maintained in 12-hour light/12-hour dark cycle.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). Spectrofotometer (Nanodrop) was used to monitor the quality of RNA. RNAs from 6 replicates were pooled and used for hybridization.

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 12h they were sacrificed.

tag: Genetic background

value: CAR/PXR deficient

tag: Strain

tag: Gender

value: male

tag: Age

value: 9-12 weeks

tag: Tissue

tag: Treatment

value: 10 mg/kg TCPOBOP

source_name: Liver, untreated CAR/PXR pool

value: PXR deficient

value: 5% DMSO in corn oil


title: Heat shock 60 min B


title: Liver_TCPOBOP_PXRKO_rep2

description: No additional data.

source_name: Liver, TCPOBOP treated

label_protocol: Lucidea Universal scorecard (GE Helthcare) was added as an universal reference for microarray experiment. 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). Spectrofotometer (Nanodrop) was used to monitor the quality of RNA.

treatment_protocol: Animals were injected i.p. with TCPOBOP (10mg/kg). After 12h they were sacrificed.

source_name: Liver, untreated PXR pool


title: Liver_TCPOBOP_WT_rep3

description: No additional data.

value: wild type

source_name: Liver, untreated WT pool


title: Liver_TCPOBOP_CARKO_rep5

description: No additional data.

value: CAR deficient

value: liver

source_name: Liver, untreated CAR pool


title: Liver_TCPOBOP_CARKO_rep6

description: No additional data.


title: Liver_TCPOBOP_PXRKO_rep3

description: No additional data.


title: Liver_TCPOBOP_CARKO_rep3

description: No additional data.


title: Liver_TCPOBOP_CARKO_rep1

description: No additional data.


title: Heat shock 0 min A


title: BG03-1

description:
1400364008F
embryonic stem cell line


title: Liver_TCPOBOP_PXRKO_rep4

description: No additional data.


title: Liver_TCPOBOP_WT_rep5

description: No additional data.


title: WA09-4

description:
1334310004C
embryonic stem cell line-isolated colonies


title: WA09-5

description:
1351945015E
embryonic stem cell line


title: WA09-3

description:
1334328027E
embryonic stem cell line-isolated colonies


title: WA09-2

description:
1334328007E
embryonic stem cell line- isolated colonies


title: WA09-1

description:
1334328026D
embryonic stem cell line-isolated colonies


title: Liver_TCPOBOP_CAR/PXR_rep4

description: No additional data.


title: Liver_TCPOBOP_CARKO_rep2

description: No additional data.

source_name: Liver. untreated CAR pool


title: Liver_TCPOBOP_WT_rep6

description: No additional data.


title: Liver_TCPOBOP_CARKO_rep4

description: No additional data.


title: Liver_TCPOBOP_CAR/PXR_rep1

description: No additional data.


title: Liver_TCPOBOP_PXRKO_rep1

description: No additional data.


title: Liver_TCPOBOP_WT_rep4

description: No additional data.

source_name: Liver TCPOBOP-treated


title: Liver_TCPOBOP_CAR/PXR_rep2

description: No additional data.


title: Liver_TCPOBOP_WT_rep1

description: No additional data.

source_name: Liver, untreated pool


title: Cocaine Regulates MEF2 to Control Synaptic and Behavioral Plasticity

status: Public on Aug 24 2008

city: Boston

first: Will

last: Renthal

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

description: These data describe the gene promoters to which MEF2 binds in the nucleus accumbens of mice treated repeatedly with cocaine.

hyb_protocol: Performed by Nimblegen (see www.nimblegen.com)

data_processing: Tukey biweight by Nimblegen

source_name: Nucleus accumbens (MEF2 enriched IP)

label_protocol: Labeling was performed as described in Sikder et al. JBC 2006

extract_protocol: Fresh NAc punches were processed for ChIP. Briefly, punches were cross-linked and lysed, and the chromatin was fragmented by sonication to an average length of 700 bp. For each sample, bilateral NAc punches were pooled from 8 mice. Aliquots of sonicated chromatin were incubated with 4 µg of MEF2A antibody and the immunoprecipitated DNA was purified, amplified by ligation-mediated PCR, and labeled to Cy3 (input) or Cy5 (MEF2 IP).

tag: Male C57/Bl6 mice, 10-12 weeks old. Treated with cocaine (20mg/kg) for 7 days and sacrificed 24hrs after the last dose.

source_name: Nucleus accumbens (input enriched)


title: Liver_PB_CAR_rep5

description: No additional data.

source_name: Liver, phenobarbital-treated

treatment_protocol: Animals were injected i.p. with phenobarbital (100mg/kg). After 12h they were sacrificed.

value: 100 mg/kg phenobarbital


title: Liver_PB_CAR_rep2

description: No additional data.

source_name: Liver, phenobarbital treated


title: Liver_PB_PXR_rep3

description: No additional data.


title: Liver_PB_PXR_rep5

description: No additional data.

source_name: Liver, untreated, PXR pool


title: Liver_PB_PXR_rep2

description: No additional data.

source_name: Liver, phenobarbital treatment


title: Liver_TCPOBOP_WT_rep2

description: No additional data.


title: Liver_PB_CAR_rep6

description: No additional data.


title: Liver_PB_CAR_rep3

description: No additional data.


title: Liver_PB_PXR_rep4

description: No additional data.


title: Liver_PB_PXR_rep6

description: No additional data.